User: hfang4

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hfang40
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Posts by hfang4

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Plotting Linkage Disequilibrium Decay Across The Genome
... I had the same problem as described by veronicaschroeder78: Error in eval(expr, envir, enclos) : object 'BP_B' not found. I solved the problem by modifying a little be in Iran's codes: change sep="\t" to sep="", others keep the same, and also change "geom_line" to "geom_point" will give you scatter ...
written 14 months ago by hfang40
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Answer: A: loop for samtools to deal with multiple files
... This final version of the script worked. Thank all for your suggestions, comments, codes and insight. #! /bin/bash cd /share/gwascotton/GBS_data/pileup_trial/ source /usr/local/apps/samtools/samtools017a.bash for i in $(ls *.bam); ...
written 19 months ago by hfang40
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Comment: C: loop for samtools to deal with multiple files
... Thanks for the scripts. I tried several files, but neither of them works. The bash one keeps running for ever and the csh one gave me the same error message "Ambiguous output redirect". ...
written 19 months ago by hfang40
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Comment: C: loop for samtools to deal with multiple files
... Thanks for the idea. I run the following codes but got another error "Ambiguous output redirect". I think we are almost there. But any idea on the new error? #! /bin/csh cd /share/gwascotton/GBS_data/pileup_trial/ source /usr/local/apps/samtools/samtools017a.csh ls *.bam > ...
written 19 months ago by hfang40 • updated 19 months ago by genomax65k
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Comment: C: loop for samtools to deal with multiple files
... Thank you for the code. I think I have to use csh because I have to submit my job to high performance computing (HPC) server and using the old version of samtools which the source code give the path to it. I modified your code a little bit as attached below, but I got error "while: Expression Synta ...
written 19 months ago by hfang40 • updated 19 months ago by genomax65k
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Comment: C: loop for samtools to deal with multiple files
... Thanks for the comments, but the link you provided can't be opened. I tried bath script. It worked somehow because it produced .pileup files, but I also got error messages “/usr/local/apps/samtools/samtools017a.csh: line2: setenv: command not found” and “/usr/local/apps/samtools/samtools017a.csh: ...
written 19 months ago by hfang40
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(Closed) loop for samtools to deal with multiple files
... Hello, I have a script to run samtools pileup for multiple files. The script worked if I ran one file at a time without loop, but it gave me error saying "Illegal variable name" with the loop. So, I think it is something wrong with the loop. I have to use the old version of samtools with the pileup ...
software error snp written 19 months ago by hfang40
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loop for samtools to deal with multiple files
... Hello, I have a script to run samtools pileup for multiple files. The script worked if I ran one file at a time without loop, but it gave me error saying "Illegal variable name" with the loop. So, I think it is something wrong with the loop. I have to use the old version of samtools with the pileup ...
software error snp written 19 months ago by hfang40

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